Happened to me too. I took it in, saying it was probably the truss rod, they said it was the tuners and messed with those. Got the bass back and he had tightened the truss rod to mask the fact that it WAS the truss rod. Tightening it obviously fixed it, but that didn't solve the grand problem as it also made made neck have virtually zero bow. Got my money back...

And it absolutely WAS the truss rod, I went piece by piece and stopped every little bit from shaking and I couldn't get it to stop, so it had to be internal. If you put your ear up to the back of the neck you hear it rattle around inside.

On one of my older cheaper basses, the spring on the intonation screw had become compressed where it was badly setup. Once I had fixed the intonation, the spring was loose and was the cause of my rattles. Ended up taking the bridge apart so I could stretch the spring a tad. All fixed.